Engineering proteins that bind, move, make and break DNA

Current Opinion in Biotechnology

Volumn 14, Issue 4, 2003, Pages 371-378

  Collins, Cynthia H ^a   Yokobayashi, Yohei ^a   Umeno, Daisuke ^a   Arnold, Frances H ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; DNA; DNA POLYMERASE; ENDONUCLEASE; NUCLEOTIDE; RECOMBINASE; ZINC FINGER PROTEIN;

AMINO ACID SEQUENCE; BIOTECHNOLOGY; DNA MODIFICATION; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; DNA STRAND BREAKAGE; DNA SYNTHESIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; MOLECULAR RECOGNITION; MUTATION; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN ENGINEERING; PROTEIN INTERACTION; REVIEW; ZINC FINGER MOTIF;

EID: 0042933802     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(03)00091-0     Document Type: Article

References (51)

1. Wharton R.P., Ptashne M. Changing the binding-specificity of a repressor by redesigning an α-helix. Nature. 316:1985;601-605.
2. Hollis M., Valenzuela D., Pioli D., Wharton R., Ptashne M. A repressor heterodimer binds to a chimeric operator. Proc. Natl. Acad. Sci. U.S.A. 85:1988;5834-5838.
3. Jana R., Hazbun T.R., Fields J.D., Mossing M.C. Single-chain λ Cro repressors confirm high intrinsic dimer-DNA affinity. Biochemistry. 37:1998;6446-6455.
4. Sieber M., Allemann R.K. Single chain dimers of MASH-1 bind DNA with enhanced affinity. Nucleic Acids Res. 26:1998;1408-1413.
5. Kuntz M.A., Shapiro D.J. Dimerizing the estrogen receptor DNA binding domain enhances binding to estrogen response elements. J. Biol. Chem. 272:1997;27949-27956.
6. Simoncsits A., Chen J.Q., Percipalle P., Wang S.L., Toro I., Pongor S. Single-chain repressors containing engineered DNA-binding domains of the phage 434 repressor recognize symmetric or asymmetric DNA operators. J. Mol. Biol. 267:1997;118-131.
7. Gates C.M., Stemmer W.P.C., Kaptein R., Schatz P.J. Affinity selective isolation of ligands from peptide libraries through display on a lac repressor 'headpiece dimer'. J. Mol. Biol. 255:1996;373-386.
8. Robinson C.R., Sauer R.T. Covalent attachment of Arc repressor subunits by a peptide linker enhances affinity for operator DNA. Biochemistry. 35:1996;109-116.
9. Percipalle P., Simoncsits A., Zakhariev S., Guarnaccia C., Sanchez R., Pongor S. Rationally designed helix-turn-helix proteins and their conformational changes upon DNA-binding. EMBO J. 14:1995;3200-3205.
10. Liang T.B., Chen J.Q., Tjornhammar M.L., Pongor S., Simoncsits A. Modular construction of extended DNA recognition surfaces: mutant DNA-binding domains of the 434 repressor as building blocks. Protein Eng. 14:2001;591-599.
11. 2 zinc finger proteins. Annu. Rev. Biochem. 70:2001;313-340.
12. Beerli R.R., Barbas C.F. III Engineering polydactyl zinc-finger transcription factors. Nat. Biotechnol. 20:2002;135-141.
13. Segal D.J., Dreier B., Beerli R.R., Barbas C.F. III Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proc. Natl. Acad. Sci. U.S.A. 96:1999;2758-2763.
14. Dreier B., Beerli R.R., Segal D.J., Flippin J.D., Barbas C.F. III Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors. J. Biol. Chem. 276:2001;29466-29478.
15. Segal D.J., Beerli R.R., Blancafort P., Dreier B., Effertz K., Huber A., Koksch B., Lund C.V., Magnenat L., Valente D.et al. Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins. Biochemistry. 42:2003;2137-2148.
16. Liu Q., Xia Z., Zhong X., Case C.C. Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J. Biol. Chem. 277:2002;3850-3856.
17. Isalan M., Klug A., Choo Y. A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nat. Biotechnol. 19:2001;656-660 This paper describes an efficient strategy for the high-throughput selection of three-finger ZFPs that can recognize arbitrary 9 bp DNA sequences, on the basis of phage display technology.
18. Sera T., Uranga C. Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. Biochemistry. 41:2002;7074-7081.
19. Sanchez J.P., Ullman C., Moore M., Choo Y., Chua N.H. Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43:2002;1465-1472.
20. Stege J.T., Guan X., Ho T., Beachy R.N., Barbas C.F. III Controlling gene expression in plants using synthetic zinc finger transcription factors. Plant J. 32:2002;1077-1086.
21. Guan X., Stege J., Kim M., Dahmani Z., Fan N., Heifetz P., Barbas C.F. III, Briggs S.P. Heritable endogenous gene regulation in plants with designed polydactyl zinc finger transcription factors. Proc. Natl. Acad. Sci. U.S.A. 99:2002;13296-13301.
22. Ordiz M.I., Barbas C.F. III, Beachy R.N. Regulation of transgene expression in plants with polydactyl zinc finger transcription factors. Proc. Natl. Acad. Sci. U.S.A. 99:2002;13290-13295.
23. Reynolds L., Ullman C., Moore M., Isalan M., West M.J., Clapham P., Klug A., Choo Y. Repression of the HIV-1 5′ LTR promoter and inhibition of HIV-1 replication by using engineered zinc-finger transcription factors. Proc. Natl. Acad. Sci. U.S.A. 100:2003;1615-1620.
24. Papworth M., Moore M., Isalan M., Minczuk M., Choo Y., Klug A. Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors. Proc. Natl. Acad. Sci. U.S.A. 100:2003;1621-1626.
25. Rebar E.J., Huang Y., Hickey R., Nath A.K., Meoli D., Nath S., Chen B., Xu L., Liang Y., Jamieson A.C.et al. Induction of angiogenesis in a mouse model using engineered transcription factors. Nat. Med. 8:2002;1427-1432.
26. Blancafort P., Magnenat L., Barbas C.F. Scanning the human genome with combinatorial transcription factor libraries. Nat. Biotechnol. 21:2003;269-274 This study demonstrates whole genome scanning for specific phenotypes using combinatorial artificial ZFP transcription factor libraries.
27. Liu P.Q., Rebar E.J., Zhang L., Liu Q., Jamieson A.C., Liang Y., Qi H., Li P.X., Chen B., Mendel M.C.et al. Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. Activation of vascular endothelial growth factor A. J. Biol. Chem. 276:2001;11323-11334.
28. Lanio T., Jeltsch A., Pingoud A. On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target. Protein Eng. 13:2000;275-281.
29. Lanio T., Jeltsch A., Pingoud A. Towards the design of rare cutting restriction endonucleases: using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude. J. Mol. Biol. 283:1998;59-69.
30. Xia G., Chen L.J., Sera T., Fa M., Schultz P.G., Romesberg F.E. Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 99:2002;6597-6602 This paper describes a clever phage display approach to select for RNA polymerase activity.
31. Samuelson J.C., Xu S.Y. Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity. J. Mol. Biol. 319:2002;673-683.
32. Seligman L.M., Chisholm K.M., Chevalier B.S., Chadsey M.S., Edwards S.T., Savage J.H., Veillet A.L. Mutations altering the cleavage specificity of a homing endonuclease. Nucleic Acids Res. 30:2002;3870-3879.
33. Chevalier B.S., Stoddard B.L. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res. 29:2001;3757-3774.
34. Chevalier B.S., Kortemme T., Chadsey M.S., Baker D., Monnat R.J., Stoddard B.L. Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell. 10:2002;895-905 An impressive protein engineering effort to construct chimeric endonucleases with novel, predicted specificities using an automated computational algorithm. The crystal structure of one of the chimeric enzymes supports the design process.
35. Mills A.A., Bradley A. From mouse to man: generating megabase chromosome rearrangements. Trends Genet. 17:2001;331-339.
36. Rodriguez C.I., Buchholz F., Galloway J., Sequerra R., Kasper J., Ayala R., Stewart A.F., Dymecki S.M. High-efficiency deleter mice show that FLPe is an alternative to Cre-loxP. Nat. Genet. 25:2000;139-140.
37. Kilby N.J., Snaith M.R., Murray J.A.H. Site-specific recombinases - tools for genome engineering. Trends Genet. 9:1993;413-421.
38. Voziyanov Y., Konieczka J.H., Stewart A.F., Jayaram M. Stepwise manipulation of DNA specificity in Flp: progressively adapting Flp to individual and combinatorial mutations in its target site. J. Mol. Biol. 326:2003;65-76 This work combines rational and evolutionary design strategies to engineer the DNA target-site specificity of Flp recombinase. A powerful double-reporter screen was used to identify mutants with altered substrate specificities.
39. Voziyanov Y., Stewart A.F., Jayaram M. A dual reporter screening system identifies the amino acid at position 82 in Flp site-specific recombinase as a determinant for target specificity. Nucleic Acids Res. 30:2002;1656-1663 This paper describes a dual reporter screen for identifying Flp recombinase variants that recognize altered target DNA sequences. One reporter gene is expressed constitutively until it is excised by a recombinase that recognizes the wild-type target sequence. A second reporter gene is constitutively expressed until it is excised by a recombinase that recognizes a novel target DNA sequence. This system was used to identify mutants with either relaxed or shifted substrate specificity. By comparing these proteins, the authors identified an amino acid that plays an important role in determining substrate specificity.
40. Santoro S.W., Schultz P.G. Directed evolution of the site specificity of Cre recombinase. Proc. Natl. Acad. Sci. U.S.A. 99:2002;4185-4190 The authors used a directed evolution strategy to identify Cre recombinase variants that recognize altered DNA target sites. In separate screens, they identified Cre mutants that recognized the novel target sites (positive screening) and variants that could not recognize the wild-type site (negative screening). A combination of positive and negative screening was required to switch specificity.
41. Rufer A.W., Sauer B. Non-contact positions impose site selectivity on Cre recombinase. Nucleic Acids Res. 30:2002;2764-2771.
42. Buchholz F., Stewart A.F. Alteration of Cre recombinase site specificity by substrate-linked protein evolution. Nat. Biotechnol. 19:2001;1047-1052.
43. Patel P.H., Suzuki M., Adman E., Shinkai A., Loeb L.A. Prokaryotic DNA polymerase I: evolution, structure, and 'base flipping' mechanism for nucleotide selection. J. Mol. Biol. 308:2001;823-837 An excellent review of the structure, catalytic mechanism, and evolution of pol I, providing a detailed discussion of the molecular basis of replication fidelity. The unexpectedly high mutability of highly conserved active-site residues in DNA polymerases is discussed in relationship to their biological functions and evolution.
44. Glick E., Vigna K.L., Loeb L.A. Mutations in human DNA polymerase eta motif II alter bypass of DNA lesions. EMBO J. 20:2001;7303-7312.
45. Shinkai A., Loeb L.A. In vivo mutagenesis by Escherichia coli DNA polymerase I - Ile709 in motif A functions in base selection. J. Biol. Chem. 276:2001;46759-46764.
46. Patel P.H., Loeb L.A. Multiple amino acid substitutions allow DNA polymerases to synthesize RNA. J. Biol. Chem. 275:2000;40266-40272.
47. Skandalis A., Loeb L.A. Enzymatic properties of rat DNA polymerase β mutants obtained by randomized mutagenesis. Nucleic Acids Res. 29:2001;2418-2426.
48. Glick E., Anderson J.P., Loeb L.A. In vitro production and screening of DNA polymerase eta mutants for catalytic diversity. Biotechniques. 33:2002;1136.
49. Glick E., Chau J.S., Vigna K.L., McCulloch S.D., Adman E.T., Kunkel T.A., Loeb L.A. Amino acid substitution at conserved tyrosine 52 alters fidelity and bypass efficiency of human polymerase H. J. Biol. Chem. 21:2003;19341-19346.
50. Tae E.J.L., Wu Y.Q., Xia G., Schultz P.G., Romesberg F.E. Efforts toward expansion of the genetic alphabet: replication of DNA with three base pairs. J. Am. Chem. Soc. 123:2001;7439-7440.
51. Ghadessy F.J., Ong J.L., Holliger P. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl. Acad. Sci. U.S.A. 98:2001;4552-4557 This paper demonstrates the use of CSR for evolving polymerase function. With a heat-stable water-in-oil emulsion system to encapsulate mutant polymerases with PCR reagents, each DNA polymerase can be amplified according to its activity. This system was used to evolve polymerases with higher thermostability or resistance to an inhibitor.